Organic fertilizer amendments reshape soil microbial communities and metabolic functions in sweet cherry production.

Introduction: Soil microorganism and metabolite-mediated root-soil interactions play a pivotal role in regulating fertilizer utilization efficiency and sweet cherry growth. Methods: Four treatment groups were established: a control group (CK, garden soil with conventional fertilization) and three amended groups (T1: sheep manure-biochar-EM inoculant; T2: chicken manure-biochar-EM inoculant; T3: biochar-EM inoculant). Results and discussion: Soil physicochemical assays indicated fertilization boosted available N, P, K and organic matter but reduced pH, with T3 yielding the greatest nutrient accumulation. By integrating high-throughput sequencing and LC-MS-based non-targeted metabolomics, we characterized the structure and diversity of root-associated bacterial and fungal communities, identified differentially abundant metabolites, annotated enriched metabolic pathways, and elucidated correlations between microorganisms and metabolites. Sequencing yielded 1,862,937 valid bacterial tags and 1,757,276 valid fungal tags, which were clustered into 11,698 bacterial ASVs and 4,011 fungal ASVs. Fertilization regimes substantially altered microbial community composition, with Pseudomonadota and Ascomycota as the dominant bacterial and fungal phyla, respectively. A total of 355 known metabolites were identified, predominantly enriched in xenobiotic biodegradation and amino acid metabolism pathways. T3 exhibited the highest number of differentially abundant metabolites (206) compared to CK, with significant enrichment in pyrimidine and phenylalanine metabolism. Correlation analysis revealed significant treatment-specific associations between key rhizosphere bacterial genera and differentially abundant metabolites (e.g., pyrimidine- and phenylalanine-pathway intermediates), with positive correlations dominating in T3 and negative correlations dominating in T2. Partial least squares path modeling (PLS-PM) further showed that fertilization affected soil metabolite accumulation predominantly through soil physicochemical properties, while the microbial-community pathway to metabolite accumulation was not statistically supported. Collectively, our findings demonstrate that fertilization exerts treatment-specific regulatory effects on root-associated microbial communities and reshapes the soil metabolome, thereby providing a theoretical basis for precision fertilization and sustainable soil management in sweet cherry orchards.